Dear Tim,
I added an optional argument sitewise to the CI and RI function in
phangorn. The vector may contains NaN if the function is undefined: pscore
of 0 for CI, uninformative site for RI.
It is now on github:
library(devtools)
install_github("KlausVigo/phangorn")
Cheers,
Klaus
On Thu, Dec 17, 2015 at 8:38 PM, Read, Timothy D <tr...@emory.edu> wrote:
> Hi all,
>
>
> I am interested in finding homoplasious sites in a nucleotide sequence
> alignment on a ML tree calculated from that alignment. Is there a commonly
> used approach for doing this in ape, phangorn etc. I have tried a number
> of google searches based around 'R homoplasy' but cant find anything.
>
>
> On a related note, is there a function available to calculate the
> consistency index for a given position on an alignment rather than an
> average for the whole alignment, which is what CI in phangorn does now?
>
>
> thanks!
>
>
> Tim
>
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